Mercurial > repos > lecorguille > xcms_plot_chromatogram
comparison xcms_plot_chromatogram.r @ 0:c749bfd3410e draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author | lecorguille |
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date | Tue, 18 Sep 2018 16:06:05 -0400 |
parents | |
children | 7c0cc7a3c3db |
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-1:000000000000 | 0:c749bfd3410e |
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1 #!/usr/bin/env Rscript | |
2 | |
3 | |
4 # ----- PACKAGE ----- | |
5 cat("\tSESSION INFO\n") | |
6 | |
7 #Import the different functions | |
8 source_local <- function(fname){ argv <- commandArgs(trailingOnly=FALSE); base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)); source(paste(base_dir, fname, sep="/")) } | |
9 source_local("lib.r") | |
10 source_local("lib-xcms3.x.x.r") | |
11 | |
12 pkgs <- c("xcms","batch","RColorBrewer") | |
13 loadAndDisplayPackages(pkgs) | |
14 cat("\n\n"); | |
15 | |
16 | |
17 # ----- ARGUMENTS ----- | |
18 cat("\tARGUMENTS INFO\n") | |
19 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects | |
20 write.table(as.matrix(args), col.names=F, quote=F, sep='\t') | |
21 | |
22 cat("\n\n") | |
23 | |
24 # ----- PROCESSING INFILE ----- | |
25 cat("\tARGUMENTS PROCESSING INFO\n") | |
26 | |
27 cat("\n\n") | |
28 | |
29 | |
30 # ----- ARGUMENTS PROCESSING ----- | |
31 cat("\tINFILE PROCESSING INFO\n") | |
32 | |
33 mergeXDataReturn <- mergeXData(args) | |
34 xdata <- mergeXDataReturn$xdata | |
35 singlefile <- mergeXDataReturn$singlefile | |
36 md5sumList <- mergeXDataReturn$md5sumList | |
37 sampleNamesList <- mergeXDataReturn$sampleNamesList | |
38 chromTIC <- mergeXDataReturn$chromTIC | |
39 chromBPI <- mergeXDataReturn$chromBPI | |
40 chromTIC_adjusted <- mergeXDataReturn$chromTIC_adjusted | |
41 chromBPI_adjusted <- mergeXDataReturn$chromBPI_adjusted | |
42 | |
43 cat("\n\n") | |
44 | |
45 | |
46 # ----- MAIN PROCESSING INFO ----- | |
47 cat("\tMAIN PROCESSING INFO\n") | |
48 | |
49 | |
50 cat("\t\tDRAW GRAPHICS\n") | |
51 | |
52 if (!is.null(chromTIC) || is.null(chromTIC)) { cat("\t\t\tCompute TIC\n"); chromTIC <- chromatogram(xdata, aggregationFun = "sum") } | |
53 if (!is.null(chromBPI) || is.null(chromBPI)) { cat("\t\t\tCompute BPI\n"); chromBPI <- chromatogram(xdata, aggregationFun = "max") } | |
54 | |
55 if (!is.null(chromTIC_adjusted)) chromTIC <- chromTIC_adjusted | |
56 if (!is.null(chromBPI_adjusted)) chromBPI <- chromBPI_adjusted | |
57 | |
58 getPlotChromatogram(chromTIC, xdata, pdfname="TICs.pdf", aggregationFun = "sum") | |
59 getPlotChromatogram(chromBPI, xdata, pdfname="BPIs.pdf", aggregationFun = "max") | |
60 | |
61 cat("\n\n") | |
62 | |
63 # ----- EXPORT ----- | |
64 | |
65 cat("\tXCMSnExp OBJECT INFO\n") | |
66 print(xdata) | |
67 cat("\n\n") | |
68 | |
69 cat("\txcmsSet OBJECT INFO\n") | |
70 # Get the legacy xcmsSet object | |
71 xset <- getxcmsSetObject(xdata) | |
72 print(xset) | |
73 cat("\n\n") | |
74 | |
75 | |
76 cat("\tDONE\n") |